iFull wwPDB X-ray Structure Validation Report ○Aug 13, 2023 – 04:13 pm BST
PDB ID : 6Y2FTitle : Crystal structure (monoclinic form) of the complex resulting from the reaction
between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate(alpha-ketoamide 13b)
Authors : Zhang, L.; Lin, D.; Sun, X.; Hilgenfeld, R.
Deposited on : 2020-02-15Resolution : 1.95 Å(reported)
This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.
We welcome your comments at validation@mail.wwpdb.org
A user guide is available athttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp
i symbol.
with specific help available everywhere you see the ○The types of validation reports are described at
http://www.wwpdb.org/validation/2017/FAQs#types.

i were used in the production of this report:
The following versions of software and data (see references ○)MolProbity
MogulXtriage (Phenix)
EDS
buster-report
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)

:::
:
:
:
:
:
:

4.02b-467
1.8.4, CSD as541be (2020)
1.13
2.35
1.1.7 (2018)20191225.v01 (using entries in the PDB archive December 25th 2019)
5.8.0158
7.0.044 (Gargrove)
Engh & Huber (2001)

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6Y2Fi
Overall quality at a glance ○The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 1.95 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in
the following graphic. The table shows the number of entries on which the scores are based.

MetricRf ree
Clashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
2580 (1.96-1.96)2705 (1.96-1.96)
2678 (1.96-1.96)
2678 (1.96-1.96)2539 (1.96-1.96)

The table below summarises the geometric issues observed across the polymeric chains and their
fit to the electron density. The red, orange, yellow and green segments of the lower bar indicate
the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality
criteria respectively. A grey segment represents the fraction of residues that are not modelled.
The numeric value for each fraction is indicated below the corresponding segment, with a dot
representing fractions <=5% The upper red bar (where present) indicates the fraction of residues
that have poor fit to the electron density. The numeric value is given above the bar.
MolChain

Length1A306

Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

Quality of chain::

Parkinson et al. (1996)
2.35

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6Y2Fi
Entry composition ○There are 4 unique types of molecules in this entry. The entry contains 2565 atoms, of which 0are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate
conformation and the Trace column contains the number of residues modelled with at most 2atoms.
• Molecule 1 is a protein called 3C-like proteinase.
MolChainResidues

1A303

Atoms
TotalCN2341 1485 398

O436

S
22

ZeroOcc

AltConf

Trace

000

• Molecule 2 is DIMETHYL SULFOXIDE (three-letter code: DMS) (formula: C2 H6 OS).

MolChainResidues

2A

1

Atoms
Total C O
42 1S1ZeroOcc

AltConf00• Molecule 3 is {tert}-butyl {N}-[1-[(2 {S})-3-cyclopropyl-1-oxidanylidene-1-[[(2 {S},3 {R})-3-oxidanyl-4-oxidanylidene-1-[(3 {S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate (three-letter
code: O6K) (formula: C31 H41 N5 O7 ) (labeled as "Ligand of Interest" by depositor).

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Mol

Chain

Residues

3A

1Total
43

Atoms
C N
31 5O
7

ZeroOcc

AltConf00• Molecule 4 is water.
MolChain

Residues

4A177

Atoms
Total O177 177

ZeroOcc

AltConf

00

6Y2F

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6Y2FiResidue-property plots ○These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The
first graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andelectron density. Residues are color-coded according to the number of geometric quality criteria
for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more.
A red dot above a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2or more consecutive residues without any outlier are shown as a green connector. Residues present
in the sample, but not in the model, are shown in grey.
• Molecule 1: 3C-like proteinase

•
•
L232
V233
A234
M235

D229

T198
T199
I200

R188

•
L167
P168

Y154

P132

N119

P108
G109

T98

•
•
T93
A94
N95

K88

Q83

•
N72
V73

S62

•
I59

E55

•
•
•
V303
T304
F305
GLNR298

D289

•

T45
S46
GLUASP
M49
L50
N51
P52

T26
L286

G23•
N277 •N274

S254

S1Q19••Chain A:

Page 64Full wwPDB X-ray Structure Validation Report

6Y2Fi
Data and refinement statistics ○Property
Space group
Cell constantsa, b, c, α, β, γResolution (Å)% Data completeness(in resolution range)
RmergeRsym< I/σ(I) > 1
Refinement program
R, Rf ree
Rf ree test set
Wilson B-factor (Å2 )Anisotropy
Bulk solvent ksol (e/Å3 ), Bsol (Å2 )L-test for twinning2
Estimated twinning fractionFo ,Fc correlation
Total number of atoms
Average B, all atoms (Å2 )

Value
C121
98.08Å 80.93Å 51.66Å
90.00◦ 114.84◦ 90.00◦
43.37 – 1.95
43.33 – 1.95
100.0 (43.37-1.95)
100.0 (43.33-1.95)
0.08(Not available)
2.07 (at 1.95Å)REFMAC 5.8.0257
0.178 , 0.219
0.187 , 0.221
1293 reflections (4.83%)
31.20.477
0.37 , 53.3
< |L| > = 0.51, < L2 > = 0.34
No twinning to report.
0.97
2565
39.0Source
Depositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
DepositorDCC
wwPDB-VP
Xtriage
Xtriage
EDS
Xtriage
XtriageEDS
wwPDB-VP
wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 6.86% of the height of the origin peak. No significant pseudotranslation is detected.

Intensities estimated from amplitudes.
Theoretical values of < |L| >, < L2 > for acentric reflections are 0.5, 0.333 respectively for untwinned datasets,and 0.375, 0.2 for perfectly twinned datasets.
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6Y2F

iModel quality ○5.1

iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section: O6K,DMS
The Z score for a bond length (or angle) is the number of standard deviations the observed value
is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an
outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
MolChain1A

Bond lengths
RMSZ #|Z| >50.74
0/2393

Bond angles
RMSZ#|Z| >50.89
1/3251 (0.0%)

There are no bond length outliers.
All (1) bond angle outliers are listed below:
Mol1ChainARes
298

TypeARG

Atoms
NE-CZ-NH2Z
5.75

Observed(o )123.18

Ideal(o )120.30

There are no chirality outliers.
There are no planarity outliers.

5.2

iToo-close contacts ○In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms
and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes within
the asymmetric unit, whereas Symm-Clashes lists symmetry-related clashes.
Mol1234All

ChainAAAAAll

Non-H
2341
443
177
2565

H(model)00000

H(added)2294
6002300

Clashes
1400114

Symm-Clashes
00000

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 3.
All (14) close contacts within the same asymmetric unit are listed below, sorted by their clash

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6Y2F

magnitude.
Atom-1Atom-2

1:A:19:GLN:HE21
1:A:19:GLN:HE21
1:A:19:GLN:NE2
1:A:23:GLY:HA3
1:A:19:GLN:NE2
1:A:19:GLN:HE21
1:A:52:PRO:HD2
1:A:72:ASN:O
1:A:229:ASP:O
1:A:95:ASN:HB3
1:A:109:GLY:HA2
1:A:83:GLN:HE21
1:A:108:PRO:HB3
1:A:167:LEU:HB3

1:A:26:THR:HG21
1:A:26:THR:CG2
1:A:26:THR:HG21
4:A:719:HOH:O
1:A:119:ASN:HD22
1:A:119:ASN:HD22
1:A:188:ARG:HG2
1:A:73:VAL:C
1:A:233:VAL:HG23
1:A:98:THR:OG1
1:A:200:ILE:HD13
1:A:88:LYS:HD2
1:A:132:PRO:HA
1:A:168:PRO:HD2

Interatomicdistance (Å)
1.33
2.05
2.08
2.05
2.05
1.59
1.98
2.56
2.19
2.20
2.02
1.86
2.01
2.02

Clashoverlap (Å)
0.94
0.70
0.67
0.55
0.55
0.48
0.45
0.43
0.43
0.42
0.42
0.41
0.41
0.41

There are no symmetry-related clashes.

5.3i
Torsion angles ○5.3.1iProtein backbone ○In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all X-ray entries followed by that with respect to entries
of similar resolution.
The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.
MolChainAnalysed

Favoured

AllowedOutliers

1A

299/306 (98%)

285 (95%)

13 (4%)

1 (0%)All (1) Ramachandran outliers are listed below:
Mol
1ChainARes73TypeVAL

Percentiles
4130

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6Y2F

iProtein sidechains ○In the following table, the Percentiles column shows the percent sidechain outliers of the chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similar
resolution.
The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

1

A

260/263 (99%)

250 (96%)

10 (4%)

Percentiles
33

21All (10) residues with a non-rotameric sidechain are listed below:
Mol111
1
111111ChainAAA
A
A
A
A
A
A
A

Res
49
55
6293
198
232
235
254
286
289

TypeMETGLU
SER
THRTHRLEU
METSER
LEU
ASP

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (7) suchsidechains are listed below:Mol
1111
111Chain
AA
A
A
A
A
A

Res
19
69
74
83
127
203
256

5.3.3

i
RNA ○Type
GLN
GLN
GLN
GLN
GLN
ASN
GLN

There are no RNA molecules in this entry.

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6Y2Fi
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

5.5iCarbohydrates ○There are no monosaccharides in this entry.

5.6

i
Ligand geometry ○2 ligands are modelled in this entry.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogul
statistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. The
Link column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.
RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).
MolType

ChainRes

Link

2
3DMS
O6K

A
A

501
502

1

Bond lengths
Counts RMSZ #|Z| > 2
3,3,30.30
046,46,46
1.45
7 (15%)

Bond angles
Counts RMSZ #|Z| > 2
3,3,30.20
057,65,65
1.84
16 (28%)In the following table, the Chirals column lists the number of chiral outliers, the number of chiral
centers analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.
’-’ means no outliers of that kind were identified.
Mol3

TypeO6K

ChainARes
502

Link
1

Chirals-Torsions
4/42/54/54

Rings
0/4/4/4

All (7) bond length outliers are listed below:
Mol3333
3
33

ChainAAAA
AAARes502502502502502502502

Type
O6K
O6K
O6K
O6K
O6K
O6K
O6K

Atoms
O25-C24
O40-C57
C42-C40
C57-C35
O25-C27
C19-N23
C24-N23

Z
5.37
2.97
2.45
-2.25
-2.20
-2.15
-2.08

Observed(Å)
1.45
1.48
1.56
1.48
1.44
1.35
1.34

Ideal(Å)
1.34
1.42
1.52
1.52
1.48
1.41
1.37

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6Y2F

All (16) bond angle outliers are listed below:Mol
333333333
333
3
333

ChainAAAAAAAAA
A
A
A
A
A
A
A

Res502502502502502502502502502502502502502502502502

Type
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K
O6K

Atoms
C57-C40-N38
O40-C57-C35
O25-C24-N23
O41-C35-N36
C21-C19-N23
C36-C20-N15
C16-N15-C21
O25-C24-O26
C27-O25-C24
O48-C47-C45
C42-C40-N38
C29-C22-C20
C18-C19-C21
O40-C57-C40
C13-N36-C35
C42-C45-C47Z-5.25-3.79
3.65
3.54
3.46-3.38-3.29-3.04
3.04
-2.87
2.79
-2.66
-2.58
2.43
2.15
2.08

Observed(o )100.16102.47114.44130.59115.46105.52119.79120.08125.66122.86113.80111.03118.82115.44125.43117.46

Ideal(o )110.03110.63108.78122.99112.30111.87122.24125.62120.99126.23110.18114.54120.30108.54122.34112.89There are no chirality outliers.
All (4) torsion outliers are listed below:
Mol
3
3
3
3

Chain
A
A
A
A

Res
502
502
502
502

Type
O6K
O6K
O6K
O6K

Atoms
C22-C20-N15-C21
C22-C20-N15-C16
N38-C40-C57-C35
N15-C20-C36-N38

There are no ring outliers.
No monomer is involved in short contacts.
The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,
bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables will
also be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.
Any bond that is central to one or more torsion angles identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identified by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identified rings is also greater than 60 degrees, then that ring is considered an outlier.
The outliers are highlighted in purple. The color gray indicates Mogul did not find sufficientequivalents in the CSD to analyse the geometry.

Page 12Full wwPDB X-ray Structure Validation Report
Ligand O6K A 502

5.7

Bond lengths

Bond angles

Torsions

Rings

i
Other polymers ○There are no such residues in this entry.

5.8i
Polymer linkage issues ○There are no chain breaks in this entry.

6Y2F

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i
Fit of model and data ○6.1

iProtein, DNA and RNA chains ○In the following table, the column labelled ‘#RSRZ> 2’ contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,
median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled ‘Q< 0.9’ lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.
MolChainAnalysed<RSRZ>

1A

303/306 (99%)

0.26#RSRZ>215 (4%) 28

39

OWAB(Å2 )Q<0.9

19, 36, 63, 104

0All (15) RSRZ outliers are listed below:
Mol111111111111111Chain
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A

Res
50
277
46
49
51
45
274
94
93
154
233
59
72
303
232

Type
LEU
ASN
SER
MET
ASN
THR
ASN
ALA
THR
TYR
VAL
ILE
ASN
VAL
LEU

RSRZ
9.0
5.6
5.1
4.4
4.4
3.9
2.8
2.7
2.7
2.6
2.6
2.5
2.2
2.2
2.2

6.2i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

6.3

i
Carbohydrates ○There are no monosaccharides in this entry.

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6Y2Fi
Ligands ○In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber defined in the chemical component dictionary. The B-factors column lists the minimum,median, 95th percentile and maximum values of B factors of atoms in the group. The column
labelled ‘Q< 0.9’ lists the number of atoms with occupancy less than 0.9.
Mol32TypeO6K
DMS

ChainA
ARes502
501

Atoms
43/43
4/4

RSCC
0.93
0.96

RSR0.130.11

B-factors(Å2 )30,40,59,63
59,75,77,81

Q<0.900The following is a graphical depiction of the model fit to experimental electron density of all
instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers
as shown on the geometry validation Tables will also be included. Each fit is shown from different
orientation to approximate a three-dimensional view.

Electron density around O6K A 502:

2mFo -DFc (at 0.7 rmsd) in graymFo -DFc (at 3 rmsd) in purple (negative)
and green (positive)

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Full wwPDB X-ray Structure Validation Reporti
Other polymers ○There are no such residues in this entry.

6Y2F